Methods of isolating microorganisms and uses thereof

Abstract

Provided herein are methods for preparing a microbiome sample for transplantation into a subject in need thereof. In particular, the methods and compositions relate to methods of repopulating the the microbiome of a subject in the treatment of gastrointestinal maladies e.g., diarrhea and/or constipation.

What is claimed is: 
     
         1 . A method for isolating a plurality of bacteria from a biological sample, the method comprising:
 (a) contacting the sample with a plurality of mannose-binding lectin (MBL) molecules, wherein the plurality of MBL molecules bind the plurality of bacteria in the sample, and   (b) washing unbound material from the plurality of MBL molecules, thereby isolating a plurality of bacteria from the sample.   
     
     
         2 . The method of  claim 1 , further comprising a step of releasing the plurality of bacteria from the plurality of MBL molecules. 
     
     
         3 . The method of  claim 1 , wherein the biological sample is a stool sample. 
     
     
         4 - 6 . (canceled) 
     
     
         7 . The method of  claim 1 , wherein the plurality of MBL molecules are bound to a substrate. 
     
     
         8 . The method of  claim 1 , further comprising a step of selecting a donor and/or obtaining a sample from a selected donor. 
     
     
         9 . The method of  claim 1 , wherein the isolated plurality of bacteria comprises viable bacteria. 
     
     
         10 . The method of  claim 1 , wherein the plurality of bacteria are released from the plurality of MBL molecules by contacting with a calcium chelating agent. 
     
     
         11 . The method of  claim 1 , wherein the biological sample or the isolated plurality of bacteria are tested for pathogens and/or allergens. 
     
     
         12 . A method for treating a subject, the method comprising: administering a composition comprising the isolated plurality of bacteria of  claim 1 , or a portion thereof, thereby treating the subject. 
     
     
         13 . The method of  claim 12 , wherein the composition further comprises a pharmaceutically acceptable carrier. 
     
     
         14 . The method of  claim 12 , wherein the isolated plurality of bacteria are administered to the subject's intestines. 
     
     
         15 - 18 . (canceled) 
     
     
         19 . The method of  claim 12 , further comprising removing or killing the existing bacteria in the subject's intestines prior to administering the isolated plurality of bacteria. 
     
     
         20 . The method of  claim 12 , wherein the treatment is for diarrhea or constipation. 
     
     
         21 . The method of  claim 20 , wherein the diarrhea is caused by pathogenic bacteria. 
     
     
         22 . The method of  claim 21 , wherein the pathogenic bacteria comprises  Clostridium difficile.    
     
     
         23 . The method of  claim 21 , wherein the pathogenic bacteria are resistant to at least one antibiotic. 
     
     
         24 . The method of  claim 20 , wherein the diarrhea is caused by  Clostridium difficile  and is a relapse of an initial  C. difficile  infection. 
     
     
         25 . The method of  claim 20 , wherein the diarrhea and/or constipation is associated with irritable bowel syndrome, Crohn's disease, or colitis. 
     
     
         26 . A composition comprising the isolated plurality of bacteria of  claim 1 , or a portion thereof. 
     
     
         27 . A pharmaceutical composition comprising a therapeutically effective amount of the isolated plurality of bacteria of  claim 1  and a pharmaceutically acceptable carrier. 
     
     
         28 - 30 . (canceled)